ArticleBiochemistry2016
Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.
Article in Biochemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.Journal of the American Chemical Society · 2026Article
- Hammerhead Ribozymes: Structural Insights, Catalytic Mechanisms, and Cutting-Edge Applications in Synthetic Biology.International journal of molecular sciences · 2025Review
- Enhanced hammerhead ribozyme turnover rates: Reevaluating therapeutic space for small catalytic RNAs.Molecular therapy. Nucleic acids · 2025Article
- Identification of Hammerhead-variant ribozyme sequences in SARS-CoV-2.Nucleic acids research · 2024Article
- Interaction of Vanadium Complexes with Proteins: Revisiting the Reported Structures in the Protein Data Bank (PDB) since 2015.Molecules (Basel, Switzerland) · 2023Review
- Biological Catalysis and Information Storage Have Relied onBiomolecules · 2023Review
- Viroids: Non-Coding Circular RNAs Able to Autonomously Replicate and Infect Higher Plants.Biology · 2023Review
- In vitro evolution of ribonucleases from expanded genetic alphabets.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes.Angewandte Chemie (Weinheim an der Bergstrasse, Germany) · 2022Article
- Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes.Angewandte Chemie (International ed. in English) · 2022Article
- Solution Structure of NPSL2, A Regulatory Element in the oncomiR-1 RNA.Journal of molecular biology · 2022Article
- Structural variants and modifications of hammerhead ribozymes targeting influenza A virus conserved structural motifs.Molecular therapy. Nucleic acids · 2022Article
- RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis.The journal of physical chemistry. B · 2022Article
- Structural Basis for Fluorescence Activation by Pepper RNA.ACS chemical biology · 2022Article
- Self-cleaving ribozymes: substrate specificity and synthetic biology applications.RSC chemical biology · 2021Review
- RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers.RNA (New York, N.Y.) · 2020Article
- Single Mutation in Hammerhead Ribozyme Favors Cleavage Activity with Manganese over Magnesium.Non-coding RNA · 2020Article
- Crucial Roles of Two Hydrated MgAngewandte Chemie (International ed. in English) · 2020Article
- The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design.RNA (New York, N.Y.) · 2020Article
- Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme.Nature chemistry · 2020Article
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2 authors.
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Abstract
The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the pKA of G12. On the basis of this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.
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